Abstract
We experimentally show that the voltage driven unzipping of long DNA duplexes by an α-hemolysin pore is sensitive to the shape of the base pairing energy landscape. Two sequences of equal global stability were investigated. The sequence with an homogeneous base pairing profile translocates faster than the one with alternative weak and strong regions. We could qualitatively account for theses observations by theoretically describing the voltage driven translocation as a biased random walk of the unzipping fork in the sequence dependent energy landscape.
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Acknowledgments
The authors thank Laurent Lacroix (MNHN) for his precious help with the melting experiments. Financial support was provided by ANR PNANO grant ANR-06-NANO-015-01.
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Viasnoff, V., Chiaruttini, N. & Bockelmann, U. Probing DNA base pairing energy profiles using a nanopore. Eur Biophys J 38, 263–269 (2009). https://doi.org/10.1007/s00249-008-0372-2
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DOI: https://doi.org/10.1007/s00249-008-0372-2